Starting phenix.real_space_refine on Fri Aug 22 20:13:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6n_37329/08_2025/8w6n_37329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6n_37329/08_2025/8w6n_37329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6n_37329/08_2025/8w6n_37329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6n_37329/08_2025/8w6n_37329.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6n_37329/08_2025/8w6n_37329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6n_37329/08_2025/8w6n_37329.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 Na 1 4.78 5 C 5110 2.51 5 N 1158 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3857 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 30, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 30, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.28 Number of scatterers: 7616 At special positions: 0 Unit cell: (91.308, 92.395, 105.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Na 1 11.00 O 1292 8.00 N 1158 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 458.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 65.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 4.145A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.611A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.581A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.865A pdb=" N TRP A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 50' Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.516A pdb=" N LEU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.701A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.728A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.520A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.612A pdb=" N SER A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 146 through 161 removed outlier: 4.230A pdb=" N ILE A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 4.146A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.538A pdb=" N ASN A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.681A pdb=" N SER A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.837A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 339 removed outlier: 4.000A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.817A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.886A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.661A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.574A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.627A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.934A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.808A pdb=" N TYR A 542 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 543' Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.642A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.054A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.544A pdb=" N THR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.820A pdb=" N PHE B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 79 through 82 removed outlier: 3.951A pdb=" N PHE B 82 " --> pdb=" O SER B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.590A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 removed outlier: 3.622A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.501A pdb=" N GLY B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N MET B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.549A pdb=" N VAL B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.542A pdb=" N GLU B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.693A pdb=" N LYS B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.610A pdb=" N GLY B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.800A pdb=" N LEU B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.632A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 removed outlier: 3.559A pdb=" N LEU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.545A pdb=" N ALA B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 4.098A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.914A pdb=" N ALA B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.590A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.601A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.619A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.670A pdb=" N SER B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Proline residue: B 503 - end of helix removed outlier: 3.612A pdb=" N ALA B 507 " --> pdb=" O PRO B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.926A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.611A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 522 " --> pdb=" O PRO B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 534 through 539 removed outlier: 4.296A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.561A pdb=" N VAL B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.735A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.809A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2166 1.34 - 1.46: 1872 1.46 - 1.58: 3712 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 7836 Sorted by residual: bond pdb=" N THR A 423 " pdb=" CA THR A 423 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.01e+00 bond pdb=" O3 SO4 B 701 " pdb=" S SO4 B 701 " ideal model delta sigma weight residual 1.499 1.457 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" O4 SO4 B 701 " pdb=" S SO4 B 701 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" O3 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" O1 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.498 1.458 0.040 2.00e-02 2.50e+03 3.95e+00 ... (remaining 7831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 10632 4.12 - 8.24: 77 8.24 - 12.36: 11 12.36 - 16.48: 0 16.48 - 20.60: 1 Bond angle restraints: 10721 Sorted by residual: angle pdb=" N ILE A 538 " pdb=" CA ILE A 538 " pdb=" C ILE A 538 " ideal model delta sigma weight residual 111.91 105.26 6.65 8.90e-01 1.26e+00 5.58e+01 angle pdb=" C ILE B 573 " pdb=" N VAL B 574 " pdb=" CA VAL B 574 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 angle pdb=" CA LEU B 545 " pdb=" CB LEU B 545 " pdb=" CG LEU B 545 " ideal model delta sigma weight residual 116.30 136.90 -20.60 3.50e+00 8.16e-02 3.46e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.67 106.60 5.07 9.50e-01 1.11e+00 2.85e+01 angle pdb=" C VAL B 113 " pdb=" N MET B 114 " pdb=" CA MET B 114 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 ... (remaining 10716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4097 17.68 - 35.36: 381 35.36 - 53.04: 50 53.04 - 70.72: 5 70.72 - 88.40: 2 Dihedral angle restraints: 4535 sinusoidal: 1697 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG B 364 " pdb=" C ARG B 364 " pdb=" N ASP B 365 " pdb=" CA ASP B 365 " ideal model delta harmonic sigma weight residual 180.00 147.58 32.42 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA TYR B 582 " pdb=" C TYR B 582 " pdb=" N PRO B 583 " pdb=" CA PRO B 583 " ideal model delta harmonic sigma weight residual 180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU B 529 " pdb=" C LEU B 529 " pdb=" N PRO B 530 " pdb=" CA PRO B 530 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 921 0.050 - 0.101: 286 0.101 - 0.151: 62 0.151 - 0.202: 18 0.202 - 0.252: 4 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 538 " pdb=" CA ILE A 538 " pdb=" CG1 ILE A 538 " pdb=" CG2 ILE A 538 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1288 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 535 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.053 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 25 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " 0.053 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO A 535 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.044 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2493 2.83 - 3.35: 6502 3.35 - 3.86: 11967 3.86 - 4.38: 14678 4.38 - 4.90: 24704 Nonbonded interactions: 60344 Sorted by model distance: nonbonded pdb=" O ILE A 93 " pdb=" OG1 THR A 97 " model vdw 2.310 3.040 nonbonded pdb=" O LEU B 498 " pdb=" OG SER B 502 " model vdw 2.312 3.040 nonbonded pdb=" O SER A 139 " pdb=" OG1 THR A 143 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR B 141 " pdb=" O3 SO4 B 701 " model vdw 2.323 3.040 nonbonded pdb=" O ALA B 59 " pdb=" OH TYR B 81 " model vdw 2.326 3.040 ... (remaining 60339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 161 or resid 233 through 309 or resid 325 throug \ h 403 or resid 418 through 588)) selection = (chain 'B' and resid 8 through 588) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.860 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7836 Z= 0.208 Angle : 0.952 20.596 10721 Z= 0.511 Chirality : 0.053 0.252 1291 Planarity : 0.010 0.104 1274 Dihedral : 13.428 88.400 2693 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.03 (0.15), residues: 959 helix: -4.80 (0.06), residues: 635 sheet: None (None), residues: 0 loop : -3.88 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 364 TYR 0.024 0.001 TYR A 514 PHE 0.020 0.001 PHE A 540 TRP 0.033 0.002 TRP A 424 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 7836) covalent geometry : angle 0.95201 (10721) hydrogen bonds : bond 0.34547 ( 247) hydrogen bonds : angle 10.37725 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.228 Fit side-chains REVERT: A 128 MET cc_start: 0.8936 (mtp) cc_final: 0.8664 (mtp) REVERT: A 338 GLN cc_start: 0.8248 (mm110) cc_final: 0.7952 (mm110) REVERT: A 480 MET cc_start: 0.8261 (ttm) cc_final: 0.8029 (ttm) REVERT: A 546 LYS cc_start: 0.8066 (mttt) cc_final: 0.7744 (mmtt) REVERT: B 430 PHE cc_start: 0.7864 (t80) cc_final: 0.7586 (t80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.0915 time to fit residues: 22.5455 Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 428 GLN B 86 HIS B 103 ASN B 160 ASN B 270 ASN B 325 GLN B 338 GLN B 490 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109977 restraints weight = 10601.968| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.55 r_work: 0.3070 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7836 Z= 0.131 Angle : 0.674 13.069 10721 Z= 0.340 Chirality : 0.043 0.149 1291 Planarity : 0.007 0.080 1274 Dihedral : 5.670 29.708 1012 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.75 % Allowed : 11.48 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.06 (0.21), residues: 959 helix: -3.19 (0.14), residues: 640 sheet: None (None), residues: 0 loop : -3.32 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 364 TYR 0.020 0.001 TYR A 514 PHE 0.015 0.001 PHE A 368 TRP 0.016 0.002 TRP A 48 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7836) covalent geometry : angle 0.67362 (10721) hydrogen bonds : bond 0.05065 ( 247) hydrogen bonds : angle 4.76130 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.291 Fit side-chains REVERT: A 128 MET cc_start: 0.8973 (mtp) cc_final: 0.8660 (mtp) REVERT: A 338 GLN cc_start: 0.8571 (mm110) cc_final: 0.8318 (mm110) REVERT: A 480 MET cc_start: 0.8688 (ttm) cc_final: 0.8362 (ttp) REVERT: A 546 LYS cc_start: 0.8112 (mttt) cc_final: 0.7737 (mttm) REVERT: B 430 PHE cc_start: 0.8114 (t80) cc_final: 0.7870 (t80) outliers start: 23 outliers final: 13 residues processed: 160 average time/residue: 0.0877 time to fit residues: 19.2678 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 73 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 325 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111476 restraints weight = 10419.873| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.45 r_work: 0.3105 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7836 Z= 0.110 Angle : 0.625 11.579 10721 Z= 0.309 Chirality : 0.041 0.145 1291 Planarity : 0.006 0.070 1274 Dihedral : 5.263 27.674 1012 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.23 % Allowed : 13.88 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.24), residues: 959 helix: -2.14 (0.18), residues: 640 sheet: None (None), residues: 0 loop : -2.99 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.017 0.001 TYR A 514 PHE 0.013 0.001 PHE A 368 TRP 0.013 0.001 TRP A 572 HIS 0.002 0.000 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7836) covalent geometry : angle 0.62510 (10721) hydrogen bonds : bond 0.03588 ( 247) hydrogen bonds : angle 4.07018 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9036 (mtp) cc_final: 0.8739 (mtp) REVERT: A 546 LYS cc_start: 0.8230 (mttt) cc_final: 0.7903 (mttm) REVERT: B 368 PHE cc_start: 0.7191 (m-80) cc_final: 0.6603 (m-80) REVERT: B 430 PHE cc_start: 0.8057 (t80) cc_final: 0.7847 (t80) REVERT: B 480 MET cc_start: 0.8249 (ttm) cc_final: 0.7816 (ttp) outliers start: 27 outliers final: 13 residues processed: 168 average time/residue: 0.0866 time to fit residues: 20.0642 Evaluate side-chains 152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 31 HIS B 234 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112929 restraints weight = 10674.925| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.71 r_work: 0.3024 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7836 Z= 0.144 Angle : 0.646 10.652 10721 Z= 0.318 Chirality : 0.043 0.148 1291 Planarity : 0.006 0.066 1274 Dihedral : 5.214 26.657 1012 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.99 % Allowed : 15.79 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.26), residues: 959 helix: -1.67 (0.19), residues: 650 sheet: None (None), residues: 0 loop : -2.86 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.017 0.001 TYR A 514 PHE 0.013 0.001 PHE A 368 TRP 0.014 0.001 TRP A 48 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7836) covalent geometry : angle 0.64556 (10721) hydrogen bonds : bond 0.03597 ( 247) hydrogen bonds : angle 3.84585 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9017 (mtp) cc_final: 0.8689 (mtp) REVERT: A 378 GLU cc_start: 0.7795 (mp0) cc_final: 0.7574 (mp0) REVERT: A 546 LYS cc_start: 0.8231 (mttt) cc_final: 0.7812 (mttm) REVERT: B 368 PHE cc_start: 0.7260 (m-80) cc_final: 0.6731 (m-80) REVERT: B 430 PHE cc_start: 0.8140 (t80) cc_final: 0.7910 (t80) REVERT: B 480 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7836 (ttp) outliers start: 25 outliers final: 19 residues processed: 156 average time/residue: 0.0791 time to fit residues: 17.1088 Evaluate side-chains 152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 chunk 60 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 157 GLN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110808 restraints weight = 10557.774| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.55 r_work: 0.3084 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7836 Z= 0.105 Angle : 0.601 10.309 10721 Z= 0.296 Chirality : 0.041 0.142 1291 Planarity : 0.006 0.065 1274 Dihedral : 4.929 25.850 1012 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.23 % Allowed : 16.63 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.27), residues: 959 helix: -1.21 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -2.72 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 237 TYR 0.019 0.001 TYR B 273 PHE 0.012 0.001 PHE A 368 TRP 0.014 0.001 TRP A 585 HIS 0.002 0.000 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7836) covalent geometry : angle 0.60058 (10721) hydrogen bonds : bond 0.02845 ( 247) hydrogen bonds : angle 3.62365 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9062 (mtp) cc_final: 0.8784 (mtp) REVERT: A 480 MET cc_start: 0.8610 (ttm) cc_final: 0.8387 (ttp) REVERT: A 546 LYS cc_start: 0.8223 (mttt) cc_final: 0.7834 (mttm) REVERT: B 368 PHE cc_start: 0.7082 (m-80) cc_final: 0.6607 (m-80) REVERT: B 430 PHE cc_start: 0.8068 (t80) cc_final: 0.7853 (t80) REVERT: B 451 GLU cc_start: 0.8252 (mp0) cc_final: 0.7925 (mp0) REVERT: B 480 MET cc_start: 0.8216 (ttm) cc_final: 0.7769 (ttp) outliers start: 27 outliers final: 16 residues processed: 163 average time/residue: 0.0723 time to fit residues: 16.8630 Evaluate side-chains 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114600 restraints weight = 10610.886| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.72 r_work: 0.3056 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7836 Z= 0.119 Angle : 0.607 9.867 10721 Z= 0.299 Chirality : 0.042 0.141 1291 Planarity : 0.005 0.067 1274 Dihedral : 4.876 25.106 1012 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.99 % Allowed : 17.94 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.27), residues: 959 helix: -0.94 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -2.65 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.012 0.001 TYR B 379 PHE 0.012 0.001 PHE A 368 TRP 0.016 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7836) covalent geometry : angle 0.60677 (10721) hydrogen bonds : bond 0.03009 ( 247) hydrogen bonds : angle 3.58527 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9051 (mtp) cc_final: 0.8741 (mtp) REVERT: A 480 MET cc_start: 0.8782 (ttm) cc_final: 0.8536 (ttp) REVERT: A 546 LYS cc_start: 0.8228 (mttt) cc_final: 0.7833 (mttm) REVERT: B 368 PHE cc_start: 0.7121 (m-80) cc_final: 0.6675 (m-80) REVERT: B 430 PHE cc_start: 0.8107 (t80) cc_final: 0.7901 (t80) REVERT: B 451 GLU cc_start: 0.8293 (mp0) cc_final: 0.7954 (mp0) REVERT: B 480 MET cc_start: 0.8287 (ttm) cc_final: 0.7819 (ttp) outliers start: 25 outliers final: 21 residues processed: 158 average time/residue: 0.0763 time to fit residues: 16.8694 Evaluate side-chains 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114828 restraints weight = 10551.996| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.72 r_work: 0.3067 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7836 Z= 0.119 Angle : 0.605 9.775 10721 Z= 0.298 Chirality : 0.042 0.139 1291 Planarity : 0.005 0.067 1274 Dihedral : 4.829 24.712 1012 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.23 % Allowed : 18.66 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.28), residues: 959 helix: -0.71 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -2.63 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.014 0.001 TYR B 379 PHE 0.012 0.001 PHE A 368 TRP 0.020 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7836) covalent geometry : angle 0.60533 (10721) hydrogen bonds : bond 0.02910 ( 247) hydrogen bonds : angle 3.54109 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9046 (mtp) cc_final: 0.8739 (mtp) REVERT: A 480 MET cc_start: 0.8793 (ttm) cc_final: 0.8560 (ttp) REVERT: A 546 LYS cc_start: 0.8237 (mttt) cc_final: 0.7848 (mttm) REVERT: B 368 PHE cc_start: 0.7170 (m-80) cc_final: 0.6719 (m-80) REVERT: B 430 PHE cc_start: 0.8057 (t80) cc_final: 0.7843 (t80) REVERT: B 480 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7791 (ttp) outliers start: 27 outliers final: 21 residues processed: 158 average time/residue: 0.0711 time to fit residues: 15.5826 Evaluate side-chains 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 28 optimal weight: 0.0370 chunk 53 optimal weight: 0.0670 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112669 restraints weight = 10643.255| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.49 r_work: 0.3105 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7836 Z= 0.103 Angle : 0.598 9.761 10721 Z= 0.294 Chirality : 0.041 0.138 1291 Planarity : 0.005 0.069 1274 Dihedral : 4.666 24.327 1012 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.99 % Allowed : 19.50 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.28), residues: 959 helix: -0.47 (0.21), residues: 649 sheet: None (None), residues: 0 loop : -2.56 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.013 0.001 TYR B 379 PHE 0.011 0.001 PHE A 368 TRP 0.023 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7836) covalent geometry : angle 0.59843 (10721) hydrogen bonds : bond 0.02571 ( 247) hydrogen bonds : angle 3.48787 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9080 (mtp) cc_final: 0.8796 (mtp) REVERT: A 546 LYS cc_start: 0.8150 (mttt) cc_final: 0.7811 (mttm) REVERT: A 580 TYR cc_start: 0.7711 (m-10) cc_final: 0.7422 (m-10) REVERT: B 118 VAL cc_start: 0.7474 (OUTLIER) cc_final: 0.7086 (p) REVERT: B 480 MET cc_start: 0.8244 (ttm) cc_final: 0.7834 (ttp) outliers start: 25 outliers final: 20 residues processed: 155 average time/residue: 0.0764 time to fit residues: 16.5160 Evaluate side-chains 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.0000 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117295 restraints weight = 10486.559| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.71 r_work: 0.3090 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7836 Z= 0.106 Angle : 0.598 9.621 10721 Z= 0.294 Chirality : 0.041 0.148 1291 Planarity : 0.005 0.067 1274 Dihedral : 4.609 24.277 1012 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.63 % Allowed : 20.22 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.28), residues: 959 helix: -0.35 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.56 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.015 0.001 TYR B 580 PHE 0.011 0.001 PHE A 368 TRP 0.027 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7836) covalent geometry : angle 0.59788 (10721) hydrogen bonds : bond 0.02613 ( 247) hydrogen bonds : angle 3.45573 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9054 (mtp) cc_final: 0.8753 (mtp) REVERT: A 546 LYS cc_start: 0.8179 (mttt) cc_final: 0.7767 (mttm) REVERT: B 118 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7169 (p) REVERT: B 480 MET cc_start: 0.8244 (ttm) cc_final: 0.7823 (ttp) outliers start: 22 outliers final: 18 residues processed: 154 average time/residue: 0.0777 time to fit residues: 16.6738 Evaluate side-chains 152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 77 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 0.0070 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114706 restraints weight = 10456.968| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.48 r_work: 0.3211 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7836 Z= 0.102 Angle : 0.591 9.659 10721 Z= 0.290 Chirality : 0.041 0.151 1291 Planarity : 0.005 0.064 1274 Dihedral : 4.441 24.198 1012 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.39 % Allowed : 20.22 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.28), residues: 959 helix: -0.22 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.58 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.015 0.001 TYR B 246 PHE 0.011 0.001 PHE A 368 TRP 0.028 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7836) covalent geometry : angle 0.59138 (10721) hydrogen bonds : bond 0.02409 ( 247) hydrogen bonds : angle 3.38941 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7973 (m-10) cc_final: 0.7745 (m-10) REVERT: A 128 MET cc_start: 0.9076 (mtp) cc_final: 0.8802 (mtp) REVERT: A 546 LYS cc_start: 0.8195 (mttt) cc_final: 0.7967 (mttm) REVERT: B 108 ILE cc_start: 0.8807 (pt) cc_final: 0.8482 (mm) REVERT: B 118 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7221 (p) REVERT: B 480 MET cc_start: 0.8244 (ttm) cc_final: 0.7906 (ttp) outliers start: 20 outliers final: 17 residues processed: 160 average time/residue: 0.0795 time to fit residues: 17.7801 Evaluate side-chains 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117652 restraints weight = 10493.328| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.70 r_work: 0.3149 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7836 Z= 0.113 Angle : 0.606 9.564 10721 Z= 0.298 Chirality : 0.042 0.146 1291 Planarity : 0.005 0.066 1274 Dihedral : 4.496 23.328 1012 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.63 % Allowed : 19.98 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.28), residues: 959 helix: -0.12 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.52 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.016 0.001 TYR B 580 PHE 0.011 0.001 PHE A 368 TRP 0.036 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7836) covalent geometry : angle 0.60622 (10721) hydrogen bonds : bond 0.02627 ( 247) hydrogen bonds : angle 3.40799 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.87 seconds wall clock time: 34 minutes 45.19 seconds (2085.19 seconds total)